Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01021736.1 Corchorus olitorius cultivar O-4 contig21769, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 5950
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30


Found at i:2508 original size:21 final size:21

Alignment explanation


    Indices: 2484--2556  Score: 69
    Period size: 21  Copynumber: 3.5  Consensus size: 21

       2474 CGCGCCACAA

                                 
       2484 CCGGCCATCCGCGCCGCCTGC
          1 CCGGCCATCCGCGCCGCCTGC

                *  *       **     
       2505 CCGGTCAGCCTGC-CTTCCT-C
          1 CCGGCCATCC-GCGCCGCCTGC

              *        *         
       2525 CCCGCCATCCGAGCCGCCTGC
          1 CCGGCCATCCGCGCCGCCTGC

                       
       2546 CCGGCCATCCG
          1 CCGGCCATCCG

       2557 TGCCATCCTC


Statistics
Matches: 38,  Mismatches: 11, Indels: 6
        0.69            0.20        0.11

Matches are distributed among these distances:
  19    1  0.03
  20   12  0.32
  21   23  0.61
  22    2  0.05

ACGTcount: A:0.07, C:0.55, G:0.25, T:0.14


Consensus pattern (21 bp):   
CCGGCCATCCGCGCCGCCTGC

Found at i:2533 original size:41 final size:42

Alignment explanation


    Indices: 2487--2567  Score: 119
    Period size: 41  Copynumber: 2.0  Consensus size: 42

       2477 GCCACAACCG

                    *             *          *        
       2487 GCCATCCGCGCCGCCTGCCCGGTCAGCC-TGCCTTCCTCCCC
          1 GCCATCCGAGCCGCCTGCCCGGCCAGCCGTGCCATCCTCCCC

                                     *              
       2528 GCCATCCGAGCCGCCTGCCCGGCCATCCGTGCCATCCTCC
          1 GCCATCCGAGCCGCCTGCCCGGCCAGCCGTGCCATCCTCC

       2568 GCGCTACCAT


Statistics
Matches: 35,  Mismatches: 4, Indels: 1
        0.88            0.10        0.03

Matches are distributed among these distances:
  41   25  0.71
  42   10  0.29

ACGTcount: A:0.07, C:0.54, G:0.22, T:0.16


Consensus pattern (42 bp):   
GCCATCCGAGCCGCCTGCCCGGCCAGCCGTGCCATCCTCCCC

Found at i:3110 original size:15 final size:14

Alignment explanation


    Indices: 3090--3119  Score: 51
    Period size: 15  Copynumber: 2.1  Consensus size: 14

       3080 ATCTCTTTAA

                           
       3090 TTTTCCTTGCATTAT
          1 TTTTCCTTG-ATTAT

                          
       3105 TTTTCCTTGATTAT
          1 TTTTCCTTGATTAT

             
       3119 T
          1 T

       3120 GCTTTGATTG


Statistics
Matches: 15,  Mismatches: 0, Indels: 1
        0.94            0.00        0.06

Matches are distributed among these distances:
  14    6  0.40
  15    9  0.60

ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63


Consensus pattern (14 bp):   
TTTTCCTTGATTAT
Done.